Cytidine deaminases include activation induced cytidine deaminase (AID) and apolipoprotein B mRNA editing enzymes, catalytic polypeptide-like (APOBEC). These enzymes are DNA mutators capable of inserting mutations into DNA and RNA by deaminating cytidine to form uridine. These enzymes play a role in antigen-driven antibody diversification processes and in an innate defense system against retroviruses. The human APOBEC family consists of 11 members: APOBEC-1 (Apo1), APOBEC-2 (Apo2), AID, APOBEC-3A, -3B, -3C, -3DE, -3F, -3G, -3H and APOBEC-4 (Apo4). Members of the APOBEC-3A family contain either single (A3A, A3C, A3H) or double (A3B, A3DE, A3F, and A3G) zinc-dependent deaminase domain (ZDD).
Attempts have been made to replace sodium bisulfite methylome sequencing (Frommer, et al., Proceedings of the National Academy of Sciences, 89.5:1827-1831 (1992)) by using AID (Larijani, et al., Molecular Immunology, 42.5:599-604 (2005)). However problems were identified with the use of native AID including: difficulties in obtaining purified active enzyme due to toxicity in non-natural host cells, incomplete conversion of cytosine to uracil arising from low activity of enzymes and substrate bias, and a lack of in vitro assays suitable for selecting AID suitable for methylome sequencing. Hence, methylome sequencing continues to be performed by sodium bisulfite sequencing despite problems associated with this method that include the use of multiple biochemical steps, an inability to distinguish methyl from hydroxymethylcytosine, the requirement for heat to denature the DNA, additional shearing of DNA into small fragments by the chemical treatment, and a limitation on the length of a DNA that can be sequenced.